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This Week in Genome Biology: Aug 10, 2016

Two researchers from Columbia University's Institute for Genomic Medicine (IGM) explore healthcare inequalities stemming from the over-representation of individuals of European descent in large-scale data collections. Using genetic disorder diagnoses as an example, the investigators examined the influence of geographic ancestry in interpretations aided by information in the Exome Aggregation Consortium dataset. Their analyses focused on nearly 6,000 individuals sequenced at IGM, including individuals with mainly European, African, Latino, East Asian, or South Asian ancestry. Overall, they saw more candidate variants in the non-European individuals, likely due in part to an incomplete understanding of the genetic variation present in these populations.

Researchers from the University of Edinburgh's Roslin Institute and elsewhere delve into the origin and spread of a community-associated clone of methicillin-resistant Staphylococcus aureus in East Asia. Using genome sequences from 120 ST59 MRSA isolates collected in Australia, the Netherlands, Taiwan, the UK, and the US, the team mapped ST59 phylogeny and uncovered parallel ST59 emergence in the US and East Asia. Those lineages subsequently had distinct expansion and antibiotic resistance trajectories, the study's authors say. "Both clones spread independently to Australia and Europe, and we found evidence of the persistence of multi-drug resistance following export from East Asia. Direct transfer of strains between Taiwan and the USA was not observed in either direction, consistent with geographic niche exclusion."

Members of the Mouse Genomes Project from the UK and the US describe findings from a deep sequencing analysis of more than a dozen inbred mouse strains. When they considered genome sequences for 13 inbred mouse strains alongside the mouse reference genome, the researchers identified roughly 27.4 million SNPs and 5 million small insertions and deletions, bringing the tally of documented inbred lab mouse variants up to around 71 million SNPs and 12 million indels. The team demonstrated that such information can help in untangling the genetics of mouse traits, from cancer susceptibility to collagen-induced arthritis susceptibility.